Advancing brain barriers RNA sequencing: guidelines from experimental design to publication
Abstract Background RNA sequencing (RNA-Seq) in its varied forms has become an indispensable tool for analyzing differential gene expression and thus characterization of specific tissues. Aiming to understand the brain barriers genetic signature, RNA seq has also been introduced in brain barriers re...
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doaj-5a307900bb7c46628a368ed0b70f18fc2020-11-25T03:46:33ZengBMCFluids and Barriers of the CNS2045-81182020-08-0117113310.1186/s12987-020-00207-2Advancing brain barriers RNA sequencing: guidelines from experimental design to publicationDavid M. F. Francisco0Luca Marchetti1Sabela Rodríguez-Lorenzo2Eduardo Frías-Anaya3Ricardo M. Figueiredo4BtRAIN NetworkPeter Winter5Ignacio Andres Romero6Helga E. de Vries7Britta Engelhardt8Rémy Bruggmann9Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of BernTheodor Kocher Institute, University of BernMS Center Amsterdam, Amsterdam Neuroscience, Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit AmsterdamSchool of Life, Health and Chemical Sciences, The Open UniversityGenXPro GmbHGenXPro GmbHSchool of Life, Health and Chemical Sciences, The Open UniversityMS Center Amsterdam, Amsterdam Neuroscience, Department of Molecular Cell Biology and Immunology, Amsterdam UMC, Vrije Universiteit AmsterdamTheodor Kocher Institute, University of BernInterfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of BernAbstract Background RNA sequencing (RNA-Seq) in its varied forms has become an indispensable tool for analyzing differential gene expression and thus characterization of specific tissues. Aiming to understand the brain barriers genetic signature, RNA seq has also been introduced in brain barriers research. This has led to availability of both, bulk and single-cell RNA-Seq datasets over the last few years. If appropriately performed, the RNA-Seq studies provide powerful datasets that allow for significant deepening of knowledge on the molecular mechanisms that establish the brain barriers. However, RNA-Seq studies comprise complex workflows that require to consider many options and variables before, during and after the proper sequencing process. Main body In the current manuscript, we build on the interdisciplinary experience of the European PhD Training Network BtRAIN ( https://www.btrain-2020.eu/ ) where bioinformaticians and brain barriers researchers collaborated to analyze and establish RNA-Seq datasets on vertebrate brain barriers. The obstacles BtRAIN has identified in this process have been integrated into the present manuscript. It provides guidelines along the entire workflow of brain barriers RNA-Seq studies starting from the overall experimental design to interpretation of results. Focusing on the vertebrate endothelial blood–brain barrier (BBB) and epithelial blood-cerebrospinal-fluid barrier (BCSFB) of the choroid plexus, we provide a step-by-step description of the workflow, highlighting the decisions to be made at each step of the workflow and explaining the strengths and weaknesses of individual choices made. Finally, we propose recommendations for accurate data interpretation and on the information to be included into a publication to ensure appropriate accessibility of the data and reproducibility of the observations by the scientific community. Conclusion Next generation transcriptomic profiling of the brain barriers provides a novel resource for understanding the development, function and pathology of these barrier cells, which is essential for understanding CNS homeostasis and disease. Continuous advancement and sophistication of RNA-Seq will require interdisciplinary approaches between brain barrier researchers and bioinformaticians as successfully performed in BtRAIN. The present guidelines are built on the BtRAIN interdisciplinary experience and aim to facilitate collaboration of brain barriers researchers with bioinformaticians to advance RNA-Seq study design in the brain barriers community.http://link.springer.com/article/10.1186/s12987-020-00207-2 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
David M. F. Francisco Luca Marchetti Sabela Rodríguez-Lorenzo Eduardo Frías-Anaya Ricardo M. Figueiredo BtRAIN Network Peter Winter Ignacio Andres Romero Helga E. de Vries Britta Engelhardt Rémy Bruggmann |
spellingShingle |
David M. F. Francisco Luca Marchetti Sabela Rodríguez-Lorenzo Eduardo Frías-Anaya Ricardo M. Figueiredo BtRAIN Network Peter Winter Ignacio Andres Romero Helga E. de Vries Britta Engelhardt Rémy Bruggmann Advancing brain barriers RNA sequencing: guidelines from experimental design to publication Fluids and Barriers of the CNS |
author_facet |
David M. F. Francisco Luca Marchetti Sabela Rodríguez-Lorenzo Eduardo Frías-Anaya Ricardo M. Figueiredo BtRAIN Network Peter Winter Ignacio Andres Romero Helga E. de Vries Britta Engelhardt Rémy Bruggmann |
author_sort |
David M. F. Francisco |
title |
Advancing brain barriers RNA sequencing: guidelines from experimental design to publication |
title_short |
Advancing brain barriers RNA sequencing: guidelines from experimental design to publication |
title_full |
Advancing brain barriers RNA sequencing: guidelines from experimental design to publication |
title_fullStr |
Advancing brain barriers RNA sequencing: guidelines from experimental design to publication |
title_full_unstemmed |
Advancing brain barriers RNA sequencing: guidelines from experimental design to publication |
title_sort |
advancing brain barriers rna sequencing: guidelines from experimental design to publication |
publisher |
BMC |
series |
Fluids and Barriers of the CNS |
issn |
2045-8118 |
publishDate |
2020-08-01 |
description |
Abstract Background RNA sequencing (RNA-Seq) in its varied forms has become an indispensable tool for analyzing differential gene expression and thus characterization of specific tissues. Aiming to understand the brain barriers genetic signature, RNA seq has also been introduced in brain barriers research. This has led to availability of both, bulk and single-cell RNA-Seq datasets over the last few years. If appropriately performed, the RNA-Seq studies provide powerful datasets that allow for significant deepening of knowledge on the molecular mechanisms that establish the brain barriers. However, RNA-Seq studies comprise complex workflows that require to consider many options and variables before, during and after the proper sequencing process. Main body In the current manuscript, we build on the interdisciplinary experience of the European PhD Training Network BtRAIN ( https://www.btrain-2020.eu/ ) where bioinformaticians and brain barriers researchers collaborated to analyze and establish RNA-Seq datasets on vertebrate brain barriers. The obstacles BtRAIN has identified in this process have been integrated into the present manuscript. It provides guidelines along the entire workflow of brain barriers RNA-Seq studies starting from the overall experimental design to interpretation of results. Focusing on the vertebrate endothelial blood–brain barrier (BBB) and epithelial blood-cerebrospinal-fluid barrier (BCSFB) of the choroid plexus, we provide a step-by-step description of the workflow, highlighting the decisions to be made at each step of the workflow and explaining the strengths and weaknesses of individual choices made. Finally, we propose recommendations for accurate data interpretation and on the information to be included into a publication to ensure appropriate accessibility of the data and reproducibility of the observations by the scientific community. Conclusion Next generation transcriptomic profiling of the brain barriers provides a novel resource for understanding the development, function and pathology of these barrier cells, which is essential for understanding CNS homeostasis and disease. Continuous advancement and sophistication of RNA-Seq will require interdisciplinary approaches between brain barrier researchers and bioinformaticians as successfully performed in BtRAIN. The present guidelines are built on the BtRAIN interdisciplinary experience and aim to facilitate collaboration of brain barriers researchers with bioinformaticians to advance RNA-Seq study design in the brain barriers community. |
url |
http://link.springer.com/article/10.1186/s12987-020-00207-2 |
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